Journal of Molecular Evolution

Article	Citations
Molecular Evolution of Malacostracan Short Wavelength Sensitive Opsins	73
Prebiotic N-(2-Aminoethyl)-Glycine (AEG)-Assisted Synthesis of Proto-RNA?	47
Correction: Analysis of Cancer-Resisting Evolutionary Adaptations in Wild Animals and Applications for Human Oncology	46
Correction: Stochastic Epigenetic Modification and Evolution of Sex Determination in Vertebrates	43
Modified Metabolism and Response to UV Radiation: Gene Expression Variations Along an Elevational Gradient in the Asiatic Toad (Bufo gargarizans)	30
Avoiding Catastrophic Mutations Accurately Predicts Amino Acid to Codon Pairing	29
Molecular Evolution of the Green-Sensitive Opsins (RH2) in Sulawesi Oryzias Species with a Single Origin	25
Extant Sequence Reconstruction: The Accuracy of Ancestral Sequence Reconstructions Evaluated by Extant Sequence Cross-Validation	24
The evolutionary path of widespread IR heteroplasmy of chloroplast genomes in the context of Rhodophyta phylogeny	23
Scaling up Functional Analyses of the G Protein-Coupled Receptor Rhodopsin	22
Unusual Evolution of Cephalopod Tryptophan Indole-Lyases	20
How Binding Affinity and Binding Specificity Map to Sequence Space	18
Embracing Complexity: Yeast Evolution Experiments Featuring Standing Genetic Variation	17
An Ultimate Question for Functional A-to-I mRNA Editing: Why Not a Genomic G?	16
Learning from the Codon Table: Convergent Recoding Provides Novel Understanding on the Evolution of A-to-I RNA Editing	16
Screening for Viruses in Pallas’s Long-Tongued Bats (Glossophaga soricina) in Brazil	16
Functional Equivalence and Conserved Sexual Dimorphism in the Gut Microbiome: A Cross-Species Meta-analysis	15
Organophosphorus Compound Formation Through the Oxidation of Reduced Oxidation State Phosphorus Compounds on the Hadean Earth	15
Evaluating Pretrained Protein Language Model Embeddings as Proxies for Functional Similarity	15
Overlaps Between CDS Regions of Protein-Coding Genes in the Human Genome: A Case Study on the NR1D1-THRA Gene Pair	14
Odorant-Binding and Chemosensory Proteins in Fig Wasps: Evolutionary Insights From Comparative Studies	14
Post-Subfunctionalization Functions of HIF-1αA and HIF-1αB in Cyprinid Fish: Fine-Tuning Mitophagy and Apoptosis Regulation Under Hypoxic Stress	14
Understanding Functional Evolution in Orthologs and Paralogs	14
MEGA 12.1: Cross-Platform Release for macOS and Linux Operating Systems	13
Evolution of Transcript Abundance is Influenced by Indels in Protein Low Complexity Regions	13

Systematic Detection of Alternative Open Reading Frames (altORFs) in Cancer Driver Genes	12
dN/dS-H, a New Test to Distinguish Different Selection Modes in Protein Evolution and Cancer Evolution	12
On the Nature of the Last Common Ancestor: A Story from its Translation Machinery	12
On Protein Loops, Prior Molecular States and Common Ancestors of Life	12
Possible Acquisition and Molecular Evolution of vpu Genes Inferred from Comprehensive Sequence Analysis of Human and Simian Immunodeficiency Viruses	11
Mapping Patterns of G-Quadruplex-Forming Sequence Conservation in Primates	11
Phylogenetic and Evolutionary Analysis of Plant Small RNA 2′-O-Methyltransferase (HEN1) Protein Family	11
Biochemical Property Based Positional Matrix: A New Approach Towards Genome Sequence Comparison	10
Type II LDH/MDH Oxidoreductases in Pacific Oyster Magallana gigas (Thunberg, 1793): Gene Organization and Expression Patterns During Development and Across Tissues	10
Conservation of Protein Kinase A Substrates in the Cnidarian Coral Spermatozoa Among Animals and Their Molecular Evolution	10
Evolution of the Metazoan Protein Domain Repertoire Revealed by a Birth-Death-Gain Model	10
Molecular Footprints on Osmoregulation-Related Genes Associated with Freshwater Colonization by Cetaceans and Sirenians	10
RNA or DNA? Revisiting the Chemical Nature of the Cenancestral Genome	10
Understanding the Origin and Evolution of Tea (Camellia sinensis [L.]): Genomic Advances in Tea	9
The Last Universal Common Ancestor of Ribosome-Encoding Organisms: Portrait of LUCA	9
Reconstructing Evolutionary Histories with Hierarchical Orthologous Groups	9
Advances in Contact Tracing: A Bayesian Framework to Improve Network and Transmission Models	9
Cystathionine Gamma-Lyase: A Potential Longevity Gene Under Selection?	9
2025 Zuckerkandl Prize	9
Evolutionary Signatures of Thermotolerance Shaped by Adaptive Admixtures in the Ghurrah Pig of India	8
Informatic Capabilities of Translation and Its Implications for the Origins of Life	8
Best Practices in Designing, Sequencing, and Identifying Random DNA Barcodes	8
Codon Usage Evolution in Viruses: Implications for Survival and Pathogenicity	8
The De Novo Emergence of Two Brain Genes in the Human Lineage Appears to be Unsupported	8
A New View of the Last Universal Common Ancestor	8
Evolution and Functional Diversification of Serine Racemase Homologs in Bacteria	8
Correction: Reconstructing Evolutionary Histories with Hierarchical Orthologous Groups	8
Reduction of Tooth Replacement Disproportionately Affects the Evolution of Enamel Matrix Proteins	8
Biothermodynamics of Hemoglobin and Red Blood Cells: Analysis of Structure and Evolution of Hemoglobin and Red Blood Cells, Based on Molecular and Empirical Formulas, Biosynthesis Reactions, and Therm	8
Evolutionary Study of Transposable Elements: Structural Characterization and Phylogenomic Profiling in Plant Genomes	8
GC Content Across Insect Genomes: Phylogenetic Patterns, Causes and Consequences	8
Decoding the Evolution and Co-Phospho-Regulatory Networks of SHROOM Proteins	7
A Law of Redundancy Compounds the Problem of Cancer and Precision Medicine	7
FEZF2 and AIRE1: An Evolutionary Trade-off in the Elimination of Auto-reactive T Cells in the Thymus	7
EasyDIVER + : An Advanced Tool for Analyzing High Throughput Sequencing Data from In Vitro Evolution of Nucleic Acids or Amino Acids	7
Correction: Sequence Divergence in Venom Genes Within and Between Montane Pitviper (Viperidae: Crotalinae: Cerrophidion) Species is Driven by Mutation–Drift Equilibrium	7
Convergent Functional Genomic Evolution Underlying Repeated Freshwater Colonization in Cetaceans	7
PAReTT: A Python Package for the Automated Retrieval and Management of Divergence Time Data from the TimeTree Resource for Downstream Analyses	7
OrthoGrafter: Rapid Identification of Orthologs from Precomputed Placement in Phylogenetic Trees	6
Deep Conservation and Unexpected Evolutionary History of Neighboring lncRNAs MALAT1 and NEAT1	6
Evidence for Multiple Independent Expansions of Fox Gene Families Within Flatworms	6
Main Factors Shaping Amino Acid Usage Across Evolution	6
Origins and Functional Significance of Eukaryotic Protein Folds	6
Correction: Principles of Molecular Evolution: Concepts from Non-equilibrium Thermodynamics for the Multilevel Theory of Learning	5
The Mystery of Cancer Resistance: A Revelation Within Nature	5
Correlated Evolution Drives Structural Convergence of Interacting Proteins	5
Evolutionary Nonindependence Between Human piRNAs and Their Potential Target Sites in Protein-Coding Genes	5
Putative MutS2 Homologs in Algae: More Goods in Shopping Bag?	5
Caspase Domain Duplication During the Evolution of Caspase-16	5
Selection Pressure Regulates the Evolution-Structure–Function Paradigm of Monocyte Chemoattractant Protein Family	5

Is the Association of the Rare rs35667974 IFIH1 Gene Polymorphism With Autoimmune Diseases a Case of RNA Epigenetics?	4
Synonymous Codons as Potential Contributors to Chromatin Stability and Gene Body Methylation in Plants	4
The Role of Selection and Migration in the Evolution of (Auto)Immunity Genes	4
User Guided Selection and Alignment of Sequence Data by GeneMatrix	4
Genomic AT Bias Coupled with Amino Acid Metabolism Modulates Codon Usage	4
Long-Term Adaptation to Galactose as a Sole Carbon Source Selects for Mutations Outside the Canonical GAL Pathway	4
APGW/AKH Precursor from Rotifer Brachionus plicatilis and the DNA Loss Model Explain Evolutionary Trends of the Neuropeptide LWamide, APGWamide, RPCH, AKH, ACP, CRZ, and GnRH Families	4
Tracking the Diversity and Chromosomal Distribution of the Olfactory Receptor Gene Repertoires of Three Anurans Species	4
A Genomic Conceptualization of Species	4
Origin of Sex-Biased Mental Disorders: Do Males and Females Experience Different Selective Regimes?	4
A Simple Evolutionary Model of Genetic Robustness After Gene Duplication	4
Concatenation, Conflict, and Complexity: Genealogical Heterogeneity Mimics Substitutional Heterogeneity for Nucleotide Model Selection	4
2022 Zuckerkandl Prize	4
Genetic Exchanges Shape the Evolutionary Diversification Among Shigella phages	4
Co-evolution of alpha-helical transmembrane protein residues: large-scale variant profiling and complete mutational landscape of 2277 known PDB entries representing 504 unique human protein sequences	4
2024 Zuckerkandl Prize	4
Quest for Orthologs in the era of Data Deluge and AI: Challenges and Innovations in Orthology Prediction and Data Integration	4
When Complex Models Fit the Wrong Mechanistic Complexity in Phylogenomic Analysis	4
How Many Factors Influence Genomic GC Content Among Prokaryotes?	4
The GFI1 Gene Family: Evolution, Structure, and Its Role in Immune Responses	4
Case Studies in the Assessment of Microbial Fitness: Seemingly Subtle Changes Can Have Major Effects on Phenotypic Outcomes	4
Replication Rate-Information Storage Trade-Off Shapes Genome Architecture Across Domains	4
A Comparative Genomics Approach to Understanding the Evolution of Olfaction in Cetaceans	3
Highly Conserved Core Residues Define Old-World Alphaviruses and Trace Early Evolutionary Divergence	3
Correction: G:U-Independent RNA Minihelix Aminoacylation by Nanoarchaeum equitans Alanyl-tRNA Synthetase: An Insight into the Evolution of Aminoacyl-tRNA Synthetases	3
NCBI Orthologs: Public Resource and Scalable Method for Computing High-Precision Orthologs Across Eukaryotic Genomes	3
Evolution of the Major Components of Innate Immunity in Animals	3
Convergent Evolution of Two Dopamine Receptor Genes: Repeated Evolution of Exon 6 Skipping in Drd2, and Repeated Deletion of Exon 6 in Drd3	3
Introduction to the Special Issue on Early Evolution and the Last Common Ancestor	3
Principles of Molecular Evolution: Concepts from Non-equilibrium Thermodynamics for the Multilevel Theory of Learning	3
On the Unknown Proteins of Eukaryotic Proteomes	3
Efficiency of Ancestral Inference and Characterization of Genetic Structure of Chinese Kazakh Group with a Novel InDel Panel	3
OrthoXML-Tools: A Toolkit for Manipulating OrthoXML Files for Orthology Data	3
A Concept of Complementarity Between Complexity and Redundancy can Account for Kant’s Biological Teleology and Unify Mechanistic and Finalistic Biology	3
A Multi-level Perspective on the Evolution of Orthologs and Their Functions	3
Recurrent Independent Pseudogenization Events of the Sperm Fertilization Gene ZP3r in Apes and Monkeys	3
First Report on Presence of Mitochondrial Introns in Freshwater Sponges, and Pseudogenic Evidence of Their Loss	3
Transcription Factor Evolution Associated with Social Transitions in Blattodea	3
Deep Dive into Evolution: How Cetaceans Adapt Their Anticoagulant Genes for Underwater Survival	3
Selection Across the Three-Dimensional Structure of Venom Proteins from North American Scolopendromorph Centipedes	3
Varying Modes of Selection Among Toxin Families in the Venoms of the Giant Desert Hairy Scorpions (Hadrurus)	3
The Abundance of Viroid-Like RNA Obelisk-S.s in Streptococcus sanguinis SK36 May Suffice for Evolutionary Persistence	3
Functionality versus Adaptation: Insights from Transcriptional Adaptation	3
Epistasis-Driven Evolution of the SARS-CoV-2 Secondary Structure	3
The Unfinished Reconstructed Nature of the Last Universal Common Ancestor	3
A Bayesian Framework for the Network Analysis of Transmission Dynamics in Infectious Disease	3
Molecular Evolution of Aryl Hydrocarbon Receptor Signaling Pathway Genes	3
Decay of Skin-Specific Gene Modules in Pangolins	3
Profylo: A Python Package for Phylogenetic Profile Comparison and Analysis	2
Functional Divergence and Origin of the Vertebrate Praja Family	2
Diversification of von Willebrand Factor A and Chitin-Binding Domains in Pif/BMSPs Among Mollusks	2
Collaborative Expression: Transcriptomics of Conus virgo Suggests Contribution of Multiple Secretory Glands to Venom Production	2
Left–Right Reversal Recurrently Evolved Regardless of Diaphanous-Related Formin Gene Duplication or Loss in Snails	2
Correction to: Evidence for Multiple Independent Expansions of Fox Gene Families Within Flatworms	2
Conservation of a Chromosome 8 Inversion and Exon Mutations Confirm Common Gulonolactone Oxidase Gene Evolution Among Primates, Including H. Neanderthalensis	2
Structural and Evolutionary Analysis of Proteins Endowed with a Nucleotidyltransferase, or Non-canonical Palm, Catalytic Domain	2
Exploring Flexibility and Folding Patterns Throughout Time in Voltage Sensors	2
Best Practices in Microbial Experimental Evolution	2
The Hypervariable Tpr Multigene Family of Theileria Parasites, Defined by a Conserved, Membrane-Associated, C-Terminal Domain, Includes Several Copies with Defined Orthology Between Species	2
Human Riboviruses: A Comprehensive Study	2
Positive Selection Shapes Breast Cancer Tumor Suppressor Genes: Unveiling Insights into BRCA1, BRCA2, and MDC1 Stability	2
Correction: Fit-Seq2.0: An Improved Software for High-Throughput Fitness Measurements Using Pooled Competition Assays	2
Resurrecting tRNAs of the Last Universal Common Ancestor (Commonote) Toward Rebuilding the Ancient Translation System	2
Stem Life: A Framework for Understanding the Prebiotic-Biotic Transition	2
Mutations Inactivating Biosynthesis of Dispensable Carbohydrate-Antigens Prevented Extinctions in Primate/Human Lineage Evolution	2
Analysis of Programmed Cell Death-1 (PD-1) Gene Variations (re11568821 and rs41386349) in HTLV-1 Infection Using One Primer Pair and Proviral Load	2
Mutation Rate Variation and Other Challenges in 2-LTR Dating of Primate Endogenous Retrovirus Integrations	2
Functional Diversification and the Plant Secondary Cell Wall	2
Nucleobases in Meteorites to Nucleobases in RNA and DNA?	2
Fit-Seq2.0: An Improved Software for High-Throughput Fitness Measurements Using Pooled Competition Assays	2
uORF-Mediated Translational Regulation of ATF4 Serves as an Evolutionarily Conserved Mechanism Contributing to Non-Small-Cell Lung Cancer (NSCLC) and Stress Response	2
Ancient Host-Virus Gene Transfer Hints at a Diverse Pre-LECA Virosphere	2
Expansion and Functional Diversification of Long-Wavelength-Sensitive Opsin in Anabantoid Fishes	2
In Silico Investigation of the Interactions Between Cotton Leaf Curl Multan Virus Proteins and the Transcriptional Gene Silencing Factors of Gossypium hirsutum L.	2
Lectin Gene Families in Three Phaseolus Species: Genome-Wide Identification, Evolutionary Analysis, Pleiotropic Effect, and Regulation Under Multiple Stress Conditions	2
nT4X and nT4M: Novel Time Non-reversible Mixture Amino Acid Substitution Models	2
The Amphibian Major Histocompatibility Complex—A Review and Future Outlook	2
Clay Minerals, Panacea or Parameter in RNA Oligomerization?	2
Fascination with RNA Editing: In the Lights of Evolution and Biology	2
Extreme Sensitivity of Fitness to Environmental Conditions: Lessons from #1BigBatch	2

Ancestral Information Analysis of Chinese Korean Ethnic Group via a Novel Multiplex DIP System	2
Revisiting the Design of the Long-Term Evolution Experiment with Escherichia coli	2
Speciation Features of Ferdinandcohnia quinoae sp. nov to Adapt to the Plant Host	2